Appion

cl2d isn't running with a virtual stack when it's parent stack is also virtual (i.e. it's the second substack made from the original). I tried both Xmipp 2 and 3. The "generate missing file" option is also failing at this second level of virtual stacks. Cl2d is fine with a non-virtual stack of the same particles.

cl2d output (/data2/log-l/appion/15sep10a/align/cl2d18):

... Time stamp: 15oct20s10
... Function name: runXmippCL2D
... Appion directory: /data2/log-l/progs/myami/appion
!!! WARNING: There is more than one appion directory in your PYTHONPATH
... Using split database
Connected to database: 'ap6'
... Committing data to database
... Querying original particles from stackid=127
... Getting stack data for stackid=127
Old stack info: 'discarding more 30S, 70S, and small dots ... 155574 particle substack with 5,23,15,31,50,41,40,34,85,87,88,94,78,62,84,107,111,110,106,121,126,125,131,152,164,187,215,204,234,236,218,217,214,211,208,221,227,230,254,253,258,259,242,243,225,246,244,256,238,241,249,285,286,270,271,267,268,266,288,305,303,302,294,274,272,306,326,307,308,309,333,334,336,337,338,339,322,316,356,354,349,344,345,357,358,360,362,373,390,404,403,384,378,376,374,393,394,395,398,420,412,409,408,427,428,430,432,435,436,437,439,441,454,452,451,445,444,507,506,485,487,482,480,402 classes excluded'
... Run directory: /data2/log-l/appion/15sep10a/align/cl2d18
!!! WARNING: directory '/data2/log-l/appion/15sep10a/align/cl2d18' already exists.
... Writing function log to: runXmippCL2D.log
... Uploading ScriptData....
... Found 40 processors on this machine
... Running Appion version 'trunk-r19211'
... Getting stack data for stackid=127
Old stack info: 'discarding more 30S, 70S, and small dots ... 155574 particle substack with 5,23,15,31,50,41,40,34,85,87,88,94,78,62,84,107,111,110,106,121,126,125,131,152,164,187,215,204,234,236,218,217,214,211,208,221,227,230,254,253,258,259,242,243,225,246,244,256,238,241,249,285,286,270,271,267,268,266,288,305,303,302,294,274,272,306,326,307,308,309,333,334,336,337,338,339,322,316,356,354,349,344,345,357,358,360,362,373,390,404,403,384,378,376,374,393,394,395,398,420,412,409,408,427,428,430,432,435,436,437,439,441,454,452,451,445,444,507,506,485,487,482,480,402 classes excluded'
... Stack 127 pixel size: 2.62
... querying one stack particle from stackid=127 on Tue Oct 20 18:10:49 2015
... creating timestamp

['/usr/local/appion/EMAN2/bin', '/data2/log-l/progs/myami/appion', '/usr/local/appion/EMAN2/lib']
connecting
lines= ['\tlibmpi.so.1 => /usr/local/openmpi-1.8.1/lib/libmpi.so.1 (0x00002b6240afc000)\n', '\tlibmpi_cxx.so.1 => /usr/local/openmpi-1.8.1/lib/libmpi_cxx.so.1 (0x00002b6240dd0000)\n', '\tlibopen-rte.so.7 => /usr/local/openmpi-1.8.1/lib/libopen-rte.so.7 (0x00002b6240ffb000)\n', '\tlibopen-pal.so.6 => /usr/local/openmpi-1.8.1/lib/libopen-pal.so.6 (0x00002b6241273000)\n']
Traceback (most recent call last):
File "/data2/log-l/progs/myami/appion/bin/runXmippCL2D.py", line 660, in <module>
cl2d.start()
File "/data2/log-l/progs/myami/appion/bin/runXmippCL2D.py", line 589, in start
a.run()
File "/data2/log-l/progs/myami/appion/appionlib/proc2dLib.py", line 45, in run
self.approc2d.checkConflicts()
File "/data2/log-l/progs/myami/appion/appionlib/proc2dLib.py", line 112, in checkConflicts
self.inputNumParticles = self.inheader['nz']
TypeError: 'NoneType' object is unsubscriptable
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Generate missing file error:

dlyumkis@bpho-bladerunner-1 cl2d18] generateMissingStack.py --projectid=6 --expid=14176 --stackid=127
Connected to database: 'ap6'
... Getting stack data for stackid=127
Old stack info: 'discarding more 30S, 70S, and small dots ... 155574 particle substack with 5,23,15,31,50,41,40,34,85,87,88,94,78,62,84,107,111,110,106,121,126,125,131,152,164,187,215,204,234,236,218,217,214,211,208,221,227,230,254,253,258,259,242,243,225,246,244,256,238,241,249,285,286,270,271,267,268,266,288,305,303,302,294,274,272,306,326,307,308,309,333,334,336,337,338,339,322,316,356,354,349,344,345,357,358,360,362,373,390,404,403,384,378,376,374,393,394,395,398,420,412,409,408,427,428,430,432,435,436,437,439,441,454,452,451,445,444,507,506,485,487,482,480,402 classes excluded'
... Querying original particles from stackid=127
connecting
... Getting stack data for stackid=127
Old stack info: 'discarding more 30S, 70S, and small dots ... 155574 particle substack with 5,23,15,31,50,41,40,34,85,87,88,94,78,62,84,107,111,110,106,121,126,125,131,152,164,187,215,204,234,236,218,217,214,211,208,221,227,230,254,253,258,259,242,243,225,246,244,256,238,241,249,285,286,270,271,267,268,266,288,305,303,302,294,274,272,306,326,307,308,309,333,334,336,337,338,339,322,316,356,354,349,344,345,357,358,360,362,373,390,404,403,384,378,376,374,393,394,395,398,420,412,409,408,427,428,430,432,435,436,437,439,441,454,452,451,445,444,507,506,485,487,482,480,402 classes excluded'
... Stack 127 pixel size: 2.62
... generating stack: '/data2/log-l/appion/15sep10a/stacks/alignsub75/start.hed' with 155574 particles
Traceback (most recent call last):
File "/data2/log-l/progs/myami/appion/bin/generateMissingStack.py", line 54, in <module>
a.run()
File "/data2/log-l/progs/myami/appion/appionlib/proc2dLib.py", line 45, in run
self.approc2d.checkConflicts()
File "/data2/log-l/progs/myami/appion/appionlib/proc2dLib.py", line 112, in checkConflicts
self.inputNumParticles = self.inheader['nz']
TypeError: 'NoneType' object is unsubscriptable